The policy of extending free school meals to all pupils for the first three years of primary school in England – announced on Tuesday by the deputy prime minister, Nick Clegg – has received a guarded welcome by some education professionals and teachers.

While few doubt the benefits of free lunches for reception, year-one and year-two pupils, questions remain over whether the money could be better spent to improve key stage 1 results at age seven.

Dale Bassett, the head of public policy at the AQA exam board, summed up the view that the millions spent on providing free lunches were millions that could be better used elsewhere in the education system.

"Two words that encapsulate the problem with £600m of universal free school meals: opportunity cost," he said.

Christine Blower, the general secretary of the National Union of Teachers, said that while the announcement of free school meals for all infants was very welcome, the looming shortages in primary school places also deserved Clegg's attention.

"He now needs to grasp the nettle of the school places crisis that is happening on his watch and put a halt to the wasteful and unnecessary free schools programme," Blower said.

There was also questions over the wider claims being made for the benefits of extending free school meals.

While a two-year pilot study of universal free school meals in Newham and Durham primary schools saw a marked improvement in attainment, it found the programme made little or no difference to pupils' school attendance, behaviour or health. That left researchers puzzling over exactly why the increased uptake of school lunches had led to improved test results at key stage 1 and 2 (at age 11).

"It is also important to note that the mechanisms underlying the improvements in attainment observed in the universal pilot are not clear," the report's authors concluded.

The study found that universal free school meals were effective at removing the stigma said to be attached to means-tested free school meals, and successfully increased take-up among those from disadvantaged households.

Universal provision was also found to be far more popular than a similar effort in Wolverhampton that simply extended means-tested free school meals to a wider number of low-income families.

The government's plan – to start in September 2014 – is more limited than the pilot study, and covers only the first three years of primary school.

"How sure are we that giving children free school meals until the age of seven leads to increased take-up of paid school meals in the junior years and beyond?" said Joe Hallgarten, the RSA's director of education.

The increase in attainment came at a cost that the pilot study estimated to be £100-£120 per pupil for a one percentage point increase in attainment at key stage 1, and £40-£60 per pupil for a similar increase at key stage 2.

In contrast, the Education Endowment Foundation's toolkit – backed by the Sutton Trust – suggests that training teachers in the use of effective pupil feedback would have similar costs at key stage 1 but with a much greater impact on results.

The study also found that even with meals freely available, only 90% of pupils ate at least one school lunch a week, while complaints increased about the quality and selection of food offered, as well as longer queues at school canteens.

For many schools, increased demand for school meals would mean upgrading school kitchens and staff to keep pace, with less than a year to do so.

Russell Hobby, general secretary of the National Association of Head Teachers, said: "We hope schools will be given the help and support they need to deliver such an ambitious and well-meaning project within a relatively tight timeframe, particularly at schools which may need adaptations and equipment to accommodate a meal service.

"Nevertheless, free school meals for all infant-age children is a bold idea and if properly rolled out we are sure it will be of enormous benefit to schools, parents and pupils."

How much it would cost to upgrade school kitchens in 16,000 maintained primary schools in England is an open question – an average cost of £2,500 per school would mean a further £40m in spending.

Economists are fond of saying that there's no such thing as a free lunch, and some arguing that the £600m could be used in ways that avoid the "deadweight loss" of free meals for children from families that would otherwise have paid.

In Durham, offering universal free school meals in primary schools cost £16.6m a year – but £7.6m, nearly half the total amount, counted as deadweight loss.